Your message dated Fri, 23 Oct 2026 15:51:31 +0000
with message-id <[email protected]>
and subject line Bug#1091721: fixed in pbseqlib 5.3.5+dfsg-13
has caused the Debian Bug report #1091721,
regarding pbsuite: autopkgtest regression in testing
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1091721: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1091721
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pbsuite
Version: 15.8.24+dfsg-8
Severity: serious
User: [email protected]
Usertags: regression
Hi Maintainer
Sometime around 2024-12-26, pbsuite's autopkgtest regressed in
testing [1]. I've copied what I hope is the relevant part of the log
below.
This regression allowed blasr/5.3.5+dfsg-7 to migrate to testing.
Regards
Graham
[1] https://ci.debian.net/packages/p/pbsuite/testing/amd64/
74s 2024-12-26 05:20:04,185 [INFO] Running /usr/bin/Honey spots
--reference lambda_modified.fasta mappingFinal.bam
74s Traceback (most recent call last):
74s File "/usr/bin/Honey", line 51, in <module>
74s parseArgs()
74s File "/usr/bin/Honey", line 48, in parseArgs
74s STAGES[args.stage](args.options)
74s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py",
line 1092, in run
74s bam = pysam.Samfile(args.bam)
74s ^^^^^^^^^^^^^^^^^^^^^^^
74s File "pysam/libcalignmentfile.pyx", line 751, in
pysam.libcalignmentfile.AlignmentFile.__cinit__
74s File "pysam/libcalignmentfile.pyx", line 956, in
pysam.libcalignmentfile.AlignmentFile._open
74s ValueError: file does not contain alignment data
--- End Message ---
--- Begin Message ---
Source: pbseqlib
Source-Version: 5.3.5+dfsg-13
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pbseqlib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated pbseqlib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 23 Oct 2026 15:42:19 +0200
Source: pbseqlib
Architecture: source
Version: 5.3.5+dfsg-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1091721
Changes:
pbseqlib (5.3.5+dfsg-13) unstable; urgency=medium
.
* Guard out-of-range reads when an anchor match list has exactly one entry
Closes: #1091721
* Remove redundant fields from d/watch
* Set upstream metadata fields: Bug-Submit.
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